| 1. |
- Bokma, Folmer, et al.
(författare)
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Unexpectedly many extinct hominins
- 2012
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Ingår i: Evolution. - Hoboken, NJ : Wiley-Blackwell. - 0014-3820 .- 1558-5646. ; 66:9, s. 2969-2974
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between splitters, who recognize over 20 hominin species, and lumpers, who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27. We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.
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| 2. |
- Höhna, Sebastian, 1983-, et al.
(författare)
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Inferring Speciation and Extinction Rates under Different Sampling Schemes
- 2011
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 28:9, s. 2577-2589
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Tidskriftsartikel (refereegranskat)abstract
- The birth-death process is widely used in phylogenetics to model speciation and extinction. Recent studies have shown that the inferred rates are sensitive to assumptions about the sampling probability of lineages. Here, we examine the effect of the method used to sample lineages. Whereas previous studies have assumed random sampling (RS), we consider two extreme cases of biased sampling: diversified sampling (DS), where tips are selected to maximize diversity and cluster sampling (CS), where sample diversity is minimized. DS appears to be standard practice, for example, in analyses of higher taxa, whereas CS may occur under special circumstances, for example, in studies of geographically defined floras or faunas. Using both simulations and analyses of empirical data, we show that inferred rates may be heavily biased if the sampling strategy is not modeled correctly. In particular, when a diversified sample is treated as if it were a random or complete sample, the extinction rate is severely underestimated, often close to 0. Such dramatic errors may lead to serious consequences, for example, if estimated rates are used in assessing the vulnerability of threatened species to extinction. Using Bayesian model testing across 18 empirical data sets, we show that DS is commonly a better fit to the data than complete, random, or cluster sampling (CS). Inappropriate modeling of the sampling method may at least partly explain anomalous results that have previously been attributed to variation over time in birth and death rates.
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| 3. |
- Milotić, Tanja, et al.
(författare)
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Dung beetle assemblages, dung removal and secondary seed dispersal : data from a large-scale, multi-site experiment in the Western Palaearctic
- 2018
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Ingår i: Frontiers of Biogeography. - : eScholarship. - 1948-6596. ; 10:1-2
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Tidskriftsartikel (refereegranskat)abstract
- By manipulating faeces during feeding and breeding, dung beetles (Coleoptera: Scarabaeidae) fulfil important ecosystem functions in terrestrial ecosystems throughout the world. In a pan-European multi-site experiment (MSE), we estimated the ecosystem functions of dung removal and secondary seed dispersal by differing combinations of dung beetle functional groups. Therefore, we classified dung beetles into five functional groups according to their body size and dung manipulation method: dwellers, large and small tunnelers, and large and small rollers. Furthermore, we set up a dung beetle sampling database containing all sampled dung beetles during the project. By identifying dung beetle specimens to the species level, we obtained a detailed insight into the dung beetle communities at each study location. By establishing experimental plots allowing and inhibiting specific combinations of functional groups in the local dung beetle assemblage from removing dung and seeds, we estimated the role of each group in dung removal and secondary seed dispersal during a 4-week period. We performed all experiments in grazed (semi-) natural grasslands, and used different dung types (cattle, horse, sheep, goat or red deer) to match the herbivore species grazing in close vicinity of each of the study areas. Simultaneously, we sampled dung beetle assemblages by using pitfalls baited with the same dung types as used in the experiments. This data paper documents two datasets collected in the framework of this MSE project. All the experiments took place between 2013 and 2016 at 17 study sites in 10 countries and 11 biogeographic zones. The entire dung beetle sampling dataset was published as a sampling event dataset at GBIF. The dataset includes the sampling results of all 17 study sites, which contain 1,050 sampling events and 4,362 occurrence records of 94 species. The second dataset contains the results of the dung removal and secondary seed dispersal experiments in which we used 11 experimental treatments and the five dung types mentioned above. This experimental results dataset holds all experimental results of the MSE project (11,537 records), and was published in the online data repository Zenodo.
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| 4. |
- Milotic, Tanja, et al.
(författare)
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Functionally richer communities improve ecosystem functioning : dung removal and secondary seed dispersal by dung beetles in the Western Palaearctic
- 2019
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Ingår i: Journal of Biogeography. - : John Wiley & Sons. - 0305-0270 .- 1365-2699. ; 46:1, s. 70-82
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Tidskriftsartikel (refereegranskat)abstract
- Aim: In several ecosystems, the diversity of functional species traits has been shown to have a stronger effect on ecosystem functioning than taxonomic diversity alone. However, few studies have explored this idea at a large geographical scale. In a multisite experiment, we unravelled the relationship between ecosystem function and functional completeness of species assemblages using dung beetles as a model group, focusing on dung removal and secondary seed dispersal.Location: Seventeen grassland locations across the Western Palaearctic.Methods: We used a randomized block design with different exclosure types to control the dung and seed removing activities of individual functional groups of the local dung beetle assemblage. We classified dung beetle species according to resource specialization and into functional groups based on dung processing behaviour (dwellers, tunnellers, rollers) and body size (small, large). Additionally, we assessed the role of other soil macro-invertebrates. By sampling the dung beetle community and measuring the remaining dung and seeds after the experiment, the impact of each functional group was estimated.Results: Dung beetle assemblages differed along a north-south and east-west gradient. Dwellers dominated northernmost sites, whereas at lower latitudes we observed more tunnellers and rollers indicating a functional shift. Resource specialists were more abundant in southern and eastern areas. Overall, functional group diversity enhanced dung removal. More dung (+46.9%) and seeds (+32.1%) were removed in the southern sites and tunnellers and rollers were more effective. At the northernmost sites, where tunnellers were scarce or absent, other soil macro-invertebrates removed the majority of dung.Main conclusions: The conservation of functionally complete dung beetle assemblages is crucial to maintain the ecosystem functions provided by dung beetles. Given the latitudinal variation in functional group diversity, it is reasonable to expect compositional changes due to climate change. These changes could lead to increased dung removal and a higher secondary seed dispersal rate in northern regions.
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| 5. |
- Mitov, Venelin, et al.
(författare)
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Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - Washington, DC United States : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:34, s. 16921-16926
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic comparative methods are widely used to understand and quantify the evolution of phenotypic traits, based on phylogenetic trees and trait measurements of extant species. Such analyses depend crucially on the underlying model. Gaussian phylogenetic models like Brownian motion and Ornstein-Uhlenbeck processes are the workhorses of modeling continuous-trait evolution. However, these models fit poorly to big trees, because they neglect the heterogeneity of the evolutionary process in different lineages of the tree. Previous works have addressed this issue by introducing shifts in the evolutionary model occurring at inferred points in the tree. However, for computational reasons, in all current implementations, these shifts are "intramodel," meaning that they allow jumps in 1 or 2 model parameters, keeping all other parameters "global" for the entire tree. There is no biological reason to restrict a shift to a single model parameter or, even, to a single type of model. Mixed Gaussian phylogenetic models (MGPMs) incorporate the idea of jointly inferring different types of Gaussian models associated with different parts of the tree. Here, we propose an approximate maximum-likelihood method for fitting MGPMs to comparative data comprising possibly incomplete measurements for several traits from extant and extinct phylogenetically linked species. We applied the method to the largest published tree of mammal species with body-and brain-mass measurements, showing strong statistical support for an MGPM with 12 distinct evolutionary regimes. Based on this result, we state a hypothesis for the evolution of the brain-body-mass allometry over the past 160 million y.
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| 6. |
- Mitov, Venelin, et al.
(författare)
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Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts
- 2020
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Ingår i: Theoretical Population Biology. - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 0040-5809 .- 1096-0325. ; 131, s. 66-78
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic comparative methods (PCMs) have been used to study the evolution of quantitative traits in various groups of organisms, ranging from micro-organisms to animal and plant species. A common approach has been to assume a Gaussian phylogenetic model for the trait evolution along the tree, such as a branching Brownian motion (BM) or an Ornstein-Uhlenbeck (OU) process. Then, the parameters of the process have been inferred based on a given tree and trait data for the sampled species. At the heart of this inference lie multiple calculations of the model likelihood, that is, the probability density of the observed trait data, conditional on the model parameters and the tree. With the increasing availability of big phylogenetic trees, spanning hundreds to several thousand sampled species, this approach is facing a two-fold challenge. First, the assumption of a single Gaussian process governing the entire tree is not adequate in the presence of heterogeneous evolutionary forces acting in different parts of the tree. Second, big trees present a computational challenge, due to the time and memory complexity of the model likelihood calculation. Here, we explore a sub-family, denoted G(LInv) , of the Gaussian phylogenetic models, with the transition density exhibiting the properties that the expectation depends Linearly on the ancestral trait value and the variance is Invariant with respect to the ancestral value. We show that G(LInv), contains the vast majority of Gaussian models currently used in PCMs, while supporting an efficient (linear in the number of nodes) algorithm for the likelihood calculation. The algorithm supports scenarios with missing data, as well as different types of trees, including trees with polytomies and non-ultrametric trees. To account for the heterogeneity in the evolutionary forces, the algorithm supports models with "shifts" occurring at specific points in the tree. Such shifts can include changes in some or all parameters, as well as the type of the model, provided that the model remains within the G(LInv) family. This contrasts with most of the current implementations where, due to slow likelihood calculation, the shifts are restricted to specific parameters in a single type of model, such as the long-term selection optima of an OU process, assuming that all of its other parameters, such as evolutionary rate and selection strength, are global for the entire tree. We provide an implementation of this likelihood calculation algorithm in an accompanying R-package called PCMBase. The package has been designed as a generic library that can be integrated with existing or novel maximum likelihood or Bayesian inference tools. (C) 2019 The Author(s). Published by Elsevier Inc.
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| 7. |
- Stadler, Tanja, et al.
(författare)
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Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa
- 2013
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 62:2, s. 220-230
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Tidskriftsartikel (refereegranskat)abstract
- Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time x(cut), and fully unresolved thereafter, so that for all subclades, stem age > x(cut) > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations.
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| 8. |
- Stadler, Tanja, et al.
(författare)
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On age and species richness of higher taxa
- 2014
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 184:4, s. 447-455
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Tidskriftsartikel (refereegranskat)abstract
- Many studies have tried to identify factors that explain differences in numbers of species between clades against the background assumption that older clades contain more species because they have had more time for diversity to accumulate. The finding in several recent studies that species richness of clades is decoupled from stem age has been interpreted as evidence for ecological limits to species richness. Here we demonstrate that the absence of a positive age-diversity relationship, or even a negative relationship, may also occur when taxa are defined based on time or some correlate of time such as genetic distance or perhaps morphological distinctness. Thus, inferring underlying processes from distributions of species across higher taxa requires caution concerning the way in which higher taxa are defined. When this definition is unclear, crown age is superior to stem age as a measure of clade age.
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| 9. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 10. |
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